The Time Machine feature in OS X has been a life-saver for numerous users, from those who want to find individual lost files or folders to those who wish to restore their systems to a previous version or state following a problematic system update or application installation. While convenient, there are some precautions to take when using Time Machine to do full system restores.
Back up changed files
If you have used your system to save data and projects before you decided to restore to your backup, be sure to run Time Machine again before restoring to save your changed files. Then, after running the restore to get back to a previous system state, you will be able to invoke Time Machine again in the restored system and locate the changed files you backed up.
Use the right disc
If you have upgraded from OS X 10.5 "Leopard" and inadvertently used your old Leopard installation DVD to run the Time Machine restore on a 10.6 installation, you will run into numerous errors, including kernel panics. Be sure to use the system disc that corresponds to your OS version.
After restoring, be sure to run a permissions fix on the boot drive. Additionally, boot into Safe Mode to clear various caches and force a drive check. You can also run system maintenance with a utility like OnyX to be sure other caches, such as the font and boot caches, are rebuilt properly. Doing this will ensure that important files are properly accessible by the system.
Keep in mind these suggestions are only applicable for full system backups. If you restore individual files and folders using Time Machine, you should not have to run permissions fixes with the one exception being if you restore any nonuser files (Application files, or system files).